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The Choices We Make is an Alternate Universe that is much like normal Undertale until the ends of a True Pacifist and Genocide Route.
Long ago, there were two all-powerful twin brothers: Fusion and Axella. Fusion, the younger twin, dreamt of order and peace. The older twin, Axella, dreamt of chaos and war. When war broke out, Axella sided with the Humans and Fusion sided with the Monsters. When the Humans won and sealed Monsters underground, Axella relished this victory. Axella was certain that no one would destroy the barrier.
Many years later, in the year 2010 A.D., a human fell into the underground. The Dreemurr family took the child in. They eventually died. In the following years, six more humans fell into the Underground. Both brothers had mixed feelings. On one hand, the monsters would be free from the Underground, on the other hand, there would be another war.
Later, in the year 2016 A.D., a human child came. They had a special power that the previous humans did not. The brothers wondered how the child would use this power. Would they free monsterkind and create a world of peace and coexistence, or would they succumb to evil and annihilate everyone in their path? Only time will tell. The child's destiny awaits.
The AU is much like normal Undertale. Enemies and puzzles get more difficult as you progress. There are distinct differences such as certain Genocide boss battles. The biggest difference is at the end of a True Pacifist and Genocide Route.
Same as regular Undertale.
The True Pacifist Route is largely the same. However, if you choose to stay with Toriel, Frisk will have a dream in their bed. They will meet Fusion, the good twin. Fusion will explain that he and his evil twin brother Axella have been watching Frisk's adventure throughout the Underground.
Fusion will congratulate Frisk on not succumbing to evil and staying on the path of virtue, no matter how far they were pushed. Fusion will say that he knew Frisk would choose Pacifism. He will then say that Frisk is worthy of being the Cosmic Protector: an embodiment of good and all that is virtuous. Fusion will explain that Frisk now has unlimited power and cannot die. He ask, "So, new Cosmic Protector. What will you do next? Revive a young prince? Bring back a scientist from some hell-void? The power is yours. I know you will use it wisely."
In the Genocide Route, monsters see that you are out to kill them all. Toriel will fight you like in a Neutral and Pacifist run, only much harder. Papyrus spares you like in Undertale, but if you attack him, he will not die. Instead he will only take a little damage and fight you, proclaiming, "VERY WELL. I THE GREAT PAPYRUS WILL STOP YOU!!" You can spare him at any time in the fight, ending it immediately and aborting the Genocide Route.
Mettaton NEO will put up a fight on the Genocide Run. Sans's fight is much harder than his regular Undertale fight. Once you get to Asgore he has absorbed the 6 Human SOULS and attack you. Once you kill Asgore you must then fight Flowey. After you kill Flowey you encounter the first human to fall into the Underground, Chara (pronounced "chara", not "kara"). The encounter with them is still the same, no battle to be had.
Once Chara crashes your game, you must reopen it and wait 10 minutes. After than you will be greeted by the evil twin Axella. He will say how he and his "goodie-two-shoes brother" have watched the Human's adventures and congratulates you on your destruction of monsterkind, saying it, "fed" him. He said that he knew you would turn to the Dark Side. Axella will then turn the Player Character into Chara - the Cosmic Destroyer. Axella will tell Chara that they now have unlimited power and cannot die. Axella will then say that Chara can destroy any world as many times as they feel like. Axella then says, "Go and kill!"